somaticPostprob: Posterior probability of clonal SNV

In ndbrown6/CNtu: Copy Number tree utilities

Posterior probability of clonal SNV

Description

Computes posterior probabilities for SNV given observed VAF, total copy numbers, allelic information and cellular fraction

Usage

pr = somaticPostprob(f_hat, n, qt, q2, alpha, w, sthetaq, e)

Arguments

f_hat	numeric vector of observed VAFs where f_hat = 0 … 1
n	integer vector of total number of reads covering mutated loci
qt	integer vector of total copy numbers
q2	integer vector of major allele counts
alpha	numeric estimate of cancer cell fraction
w	list of numeric mixture weights
sthetaq	numeric vector
e	numeric error rate where e = 0 … 1

Value

list of two as follows:

ppr

data frame of posterior probabilities with following column description: Pr_somatic_clonal: probability that SNV is somatic and strictly clonal Pr_germline: probability that SNV is a germline mutation Pr_subclonal: probability that SNV is somatic and subclonal Pr_subclonal_wt0: probability that SNV is subclonal when qt = 1, 0 otherwise Pr_wt0: probability that q2 copies are mutated if locus has uniparental allele (qt = q2), 0 otherwise Pr_ge2: warning: undocumented \& not in use Pr_GL_som_HZ_alt: warning: undocumented \& not in use Pr_GL_som_HZ_ref: warning: undocumented \& not in use Pr_cryptic_SCNA: warning: undocumented LL: log likelihood sq: most probable number of mutated copies where sq = 1 ldots q2 Pr_somatic: probability that SNV is somatic i.e. Pr_somatic_clonal + Pr_subclonal

som_mut_Q_tab

list of numeric mixture weights

Note

This functionality has been lifted straight from ABSOLUTE with the unfortunate caveat that most of it is undocumented

Author(s)

David Brown
[e-mail]

ndbrown6/CNtu documentation built on March 16, 2023, 1:01 a.m.